All Jobs Error Out

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All Jobs Error Out

Yip, Miu ki
Hi all,

This afternoon, our local instance of Galaxy suddenly started producing errors for all jobs. This is the trace that gets printed out. Not sure what is happening because the error doesn’t give much information other than python not being able to find a module.

Traceback (most recent call last):
  File "/localdata1/galaxy/database/jobs_directory/002/2931/set_metadata_LMpe2m.py", line 1, in
    from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata()
  File "/localdata1/galaxy/lib/galaxy_ext/metadata/set_metadata.py", line 25, in
    import galaxy.model.mapping  # need to load this before we unpickle, in order to setup properties assigned by the mappers
  File "/localdata1/galaxy/lib/galaxy/model/mapping.py", line 19, in
    from galaxy.model.custom_types import JSONType, MetadataType, TrimmedString, UUIDType
  File "/localdata1/galaxy/lib/galaxy/model/custom_types.py", line 13, in
    from galaxy import app
  File "/localdata1/galaxy/lib/galaxy/app.py", line 17, in
    from galaxy.visualization.plugins.registry import VisualizationsRegistry
  File "/localdata1/galaxy/lib/galaxy/visualization/plugins/registry.py", line 15, in
    from galaxy.visualization.plugins import plugin as vis_plugins
  File "/localdata1/galaxy/lib/galaxy/visualization/plugins/plugin.py", line 13, in
    from galaxy.web.base import interactive_environments
  File "/localdata1/galaxy/lib/galaxy/web/base/interactive_environments.py", line 14, in
    from galaxy.tools.deps.docker_util import DockerVolume
  File "/localdata1/galaxy/lib/galaxy/tools/__init__.py", line 60, in
    import tool_shed.util.repository_util as repository_util
  File "/localdata1/galaxy/lib/tool_shed/util/repository_util.py", line 16, in
    from tool_shed.util import hg_util
  File "/localdata1/galaxy/lib/tool_shed/util/hg_util.py", line 11, in
    from mercurial.exchange import readbundle
  File "/lib64/python2.7/site-packages/mercurial/exchange.py", line 18, in
    from . import (
  File "/lib64/python2.7/site-packages/mercurial/bundle2.py", line 168, in
    urlerr = util.urlerr
AttributeError: 'module' object has no attribute 'urlerr'

Could anyone provide any insight on the issue? Thanks!
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Re: All Jobs Error Out

John Chilton-4
Did you figure this out?

It looks like you jobs are not detecting Galaxy's virtualenv and so
they are getting a dependency (in this case mercurial) from Galaxy
root packages.

I'd review this document:
https://docs.galaxyproject.org/en/master/admin/framework_dependencies.html#galaxy-job-handlers

If you still have problems and that doesn't give you any ideas -
perhaps share your job_conf.xml.

-John


On Tue, Mar 7, 2017 at 5:14 PM, Yip, Miu ki <[hidden email]> wrote:

> Hi all,
>
> This afternoon, our local instance of Galaxy suddenly started producing errors for all jobs. This is the trace that gets printed out. Not sure what is happening because the error doesn’t give much information other than python not being able to find a module.
>
> Traceback (most recent call last):
>   File "/localdata1/galaxy/database/jobs_directory/002/2931/set_metadata_LMpe2m.py", line 1, in
>     from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata()
>   File "/localdata1/galaxy/lib/galaxy_ext/metadata/set_metadata.py", line 25, in
>     import galaxy.model.mapping  # need to load this before we unpickle, in order to setup properties assigned by the mappers
>   File "/localdata1/galaxy/lib/galaxy/model/mapping.py", line 19, in
>     from galaxy.model.custom_types import JSONType, MetadataType, TrimmedString, UUIDType
>   File "/localdata1/galaxy/lib/galaxy/model/custom_types.py", line 13, in
>     from galaxy import app
>   File "/localdata1/galaxy/lib/galaxy/app.py", line 17, in
>     from galaxy.visualization.plugins.registry import VisualizationsRegistry
>   File "/localdata1/galaxy/lib/galaxy/visualization/plugins/registry.py", line 15, in
>     from galaxy.visualization.plugins import plugin as vis_plugins
>   File "/localdata1/galaxy/lib/galaxy/visualization/plugins/plugin.py", line 13, in
>     from galaxy.web.base import interactive_environments
>   File "/localdata1/galaxy/lib/galaxy/web/base/interactive_environments.py", line 14, in
>     from galaxy.tools.deps.docker_util import DockerVolume
>   File "/localdata1/galaxy/lib/galaxy/tools/__init__.py", line 60, in
>     import tool_shed.util.repository_util as repository_util
>   File "/localdata1/galaxy/lib/tool_shed/util/repository_util.py", line 16, in
>     from tool_shed.util import hg_util
>   File "/localdata1/galaxy/lib/tool_shed/util/hg_util.py", line 11, in
>     from mercurial.exchange import readbundle
>   File "/lib64/python2.7/site-packages/mercurial/exchange.py", line 18, in
>     from . import (
>   File "/lib64/python2.7/site-packages/mercurial/bundle2.py", line 168, in
>     urlerr = util.urlerr
> AttributeError: 'module' object has no attribute 'urlerr'
>
> Could anyone provide any insight on the issue? Thanks!
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
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Re: All Jobs Error Out

Yip, Miu ki
Hi John,

Thanks for the reply. I saw in the stack trace that there was a issue with mercurial, which was recently installed in the system. After uninstalling it, everything ran again. Not entirely sure what happened.

Thanks,
Miuki
On Mar 14, 2017, at 8:27 AM, John Chilton <[hidden email]<mailto:[hidden email]>> wrote:

https://docs.galaxyproject.org/en/master/admin/framework_dependencies.html#galaxy-job-handlers

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